Lysosomes are acidic, membrane-delimited organelles whose central function is to degrade macromolecules. The lysosome contains a wide variety of soluble enzymes that hydrolyze substrates as well as transmembrane proteins that perform a number of functions including transport of degradation products out of this organelle. The importance of lysosomal proteins in normal cellular physiology is illustrated by the dozens of lysosomal storage disorders (LSDs) such as Tay-Sach's disease where a deficiency in a single lysosomal protein results in accumulation of catabolites and a depletion of downstream metabolites. These monogenic diseases typically cause severe illness including mental retardation, developmental deformities, and premature death. The gene defects in over 40 different LSDs have been identified, which, through genetic counseling, has greatly decreased the prevalence of some of these disorders. Despite this impressive progress, much remains to be accomplished as there are a number of clinically-defined disorders that appear to be LSDs but which are of unknown molecular etiology. In addition, there are numerous individuals that have LSDs based upon clinical and ultrastructural criteria for which the gene defects have not been identified. We hypothesize that many of these unsolved genetic diseases are caused by mutations in genes encoding lysosomal proteins. The overall goal of this proposal is to determine the basis of these unsolved LSD cases. There are two specific aims. Aim 1 is to use a newly developed comparative proteomics method to identify aberrant proteins and the gene defects underlying numerous unsolved LSDs. Aim 2 is to use quantitative mass spectrometry with subcellular fractionation to define the lysosomal proteome and to make this information readily accessible to the biomedical community. This will establish a resource that will greatly facilitate identification of lysosomal disease genes using other approaches such as linkage analysis. Completion of these specific aims will identify new lysosomal disease genes as well as new mutations in existing disease genes that cause atypical clinical presentations. This will be of paramount significant to the affected individuals and families, and will provide important information on how lysosomal deficiencies are manifested. In addition, the proteomics methods established to investigate LSDs will enable future studies on widespread human disorders where lysosomal changes may be important, including cancer and Alzheimer disease. Finally, assignment of the lysosomal proteome will be an important contribution to functional genomics and will have broad biomedical impact.The proposed research is to determine the basis for previously unsolved human genetic diseases. This research will also establish systems for the investigation of the role of a group of biomedically important proteins in widespread human diseases in such as Alzheimer's and cancer.